Here are some things to think about.
If your bed smells like urine already, (its a really hard smell to get out) then that could be a reason why she goes back. If her litter box is in the basement and she like to hang out on the second floor, your bed is much closer.
Your version of a clean box and her idea of a clean box might not be a the same. My cat wants her box cleaned daily, might accept every second day but heaven help you if you leave it any longer. Does she use the box at all?
You say you know why she's doing it but can't live your life around what she thinks is right... What do you mean? You figure she's protesting about not being able to go outside?
You need to give more info about the details of the problem so you can get a better response... You aren't giving us much to work with
